AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA: positive energies during nmode

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 16 2006 - 11:10:29 CDT

On Wed, Aug 16, 2006, Zu Thur Yew wrote:
>
> I tried to do nmode via the MMPBSA scripts with my system of 561
> residues, but the energy's +ve after 3000 steps (4 x 10^2). The snapshot
> used was extracted after 100ps of equilibration. My colleague has
> noticed something similar with snapshots extracted across a 10ns MD run.
> Amber was re-compiled to accommodate the large system size.

There is not enough information here to know if you have a problem or not.
Per se, a positive energy is not necessarily a problem--it depends on the
system. Since you modified the code, you should certainly make sure that
sander and nmode give the same energies, and the same general minimization
behavior.

>
> Looking at the minimizations done before MD runs, the energy drops to
> -ve values within 500 steps or so and the MM energies for the snapshot
> is -ve as well.

I do not understand what you are saying here. If the "energy of the snapshot"
is negative, but the minimized(?) energy is positive, something is clearly not
working correctly. If you are not clear about what is going on, be sure to
work with smaller systems first: 561 residues is an enormous side for normal
mode analysis.

....dac
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